I haven't seen or done this, but would suspect that you would want to avoid stacking them directly on top of each other, so the bottom boat would be supporting the top.
I would suggest looking into making a rack that the bottom boat would slide under, and would carry the weight of the top boat. The material/design used would depend on how far you are hauling the boats and what the driving conditions are.
Another consideration is if you want the rack permanent or removable.
One final thought, I've seen roof racks for Kayaks that tilt them on their sides, about a 45 degree angle, when the boats are wider than the roof rack. This is also an option, but care has to be taken to not damage the hulls.
Hope some of these comments help.